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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ), 'gf_id' => 'HOM05D001546', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001546' ), 'data_identifier' => 'HOM05D001546', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001546', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '413', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01460' => 'bna', 'A05p05300' => 'bna', 'A05p05310' => 'bna', 'A07p25200' => 'bna', 'A08p14380' => 'bna', 'A09p52910' => 'bna', 'Aa31LG10G15000' => 'aar', 'Aa31LG1G26810' => 'aar', 'Aa31LG1G26820' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5141' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.594' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.193' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2864' => 'aag', 'Actinidia12247' => 'ach', 'Actinidia12248' => 'ach', 'Actinidia12249' => 'ach', 'Actinidia13562' => 'ach', 'Actinidia25026' => 'ach', 'Actinidia25027' => 'ach', 'Actinidia31396' => 'ach', 'Actinidia31397' => 'ach', 'Actinidia35664' => 'ach', 'Actinidia35665' => 'ach', 'Ah.05g174410' => 'amhyb', 'Ah.05g176670' => 'amhyb', 'Ah.07g208120' => 'amhyb', 'Ah.13g067350' => 'amhyb', 'AL4G44380' => 'aly', 'AL5G43060' => 'aly', 'Aqoxy1G01200' => 'aox', 'Aqoxy7G00662' => 'aox', 'Aqoxy7G00663' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5GPW5B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6GCE7S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8F004F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A52I0E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KRWE0T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N7BB1S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y484AZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZAG0TB' => 'arhy', 'AT2G45280' => 'ath', 'AT2G45290' => 'ath', 'AT3G60750' => 'ath', 'ATR0680G141' => 'atr', 'ATR0680G225' => 'atr', 'ATR0680G392' => 'atr', 'ATR0730G032' => 'atr', 'ATR0757G033' => 'atr', 'Atru.chr12.808' => 'acertr', 'Atru.chr5.288' => 'acertr', 'Atru.chr5.289' => 'acertr', 'AUR62004193' => 'cqu', 'AUR62004194' => 'cqu', 'AUR62013651' => 'cqu', 'AUR62016117' => 'cqu', 'AUR62041384' => 'cqu', 'BcaB02g07401' => 'bca', 'BcaB02g08944' => 'bca', 'BcaB02g09107' => 'bca', 'BcaB02g10315' => 'bca', 'BcaB08g34936' => 'bca', 'BcaC02g10176' => 'bca', 'BcaC02g12228' => 'bca', 'BcaC02g12229' => 'bca', 'BcaC05g25952' => 'bca', 'BcaC07g40594' => 'bca', 'BcaC07g42635' => 'bca', 'BcaC08g45079' => 'bca', 'BcaC08g45082' => 'bca', 'BNapus_Darmor_BZH_scaffold_170p00010' => 'bna', 'BolC4t22247H' => 'bol', 'BolC4t24747H' => 'bol', 'BolC5t30603H' => 'bol', 'BolC6t37862H' => 'bol', 'BolC6t37865H' => 'bol', 'BolC8t51159H' => 'bol', 'BraA04t15864Z' => 'bra', 'BraA05t19499Z' => 'bra', 'BraA05t19500Z' => 'bra', 'BraA07t30162Z' => 'bra', 'BraA09t40723Z' => 'bra', 'C04p06210' => 'bna', 'C04p06220' => 'bna', 'C04p31940' => 'bna', 'C04p48920' => 'bna', 'C05p19020' => 'bna', 'C06p26880' => 'bna', 'C06p26910' => 'bna', 'C08p35680' => 'bna', 'CAN.G149.33' => 'can', 'CAN.G192.10' => 'can', 'CAN.G239.11' => 'can', 'CAN.G270.15' => 'can', 'CAN.G295.12' => 'can', 'CAN.G72.4' => 'can', 'CANSAT56G2679' => 'cansat', 'CANSAT56G2954' => 'cansat', 'CANSAT56G4308' => 'cansat', 'CARHR140490' => 'chi', 'CARHR171140' => 'chi', 'CARHR248160' => 'chi', 'Carub.0004s2788' => 'cru', 'Carub.0004s2792' => 'cru', 'Carub.0005s2748' => 'cru', 'Carub.0006s3711' => 'cru', 'Ca_11345_v3' => 'car', 'Ca_19947_v3' => 'car', 'Ca_19952_v3' => 'car', 'Ca_28888_v3' => 'car', 'Ca_29061_v3' => 'car', 'CBR_g21246' => 'cbr', 'CBR_g21248' => 'cbr', 'CBR_g29371' => 'cbr', 'Cc02_g11220' => 'ccan', 'Cc02_g24060' => 'ccan', 'Cc02_g24070' => 'ccan', 'CDE04G0759' => 'cde', 'CDE04G2074' => 'cde', 'CDE09G0499' => 'cde', 'CDE11G0940' => 'cde', 'CDE12G0005' => 'cde', 'CDE12G0107' => 'cde', 'Cfa001674' => 'cfa', 'Cfa001750' => 'cfa', 'Cfa001751' => 'cfa', 'Cfa022492' => 'cfa', 'Ciclev10018991m.g' => 'ccl', 'Ciclev10021754m.g' => 'ccl', 'Ciclev10033603m.g' => 'ccl', 'CiPaw.01G263500' => 'cil', 'CiPaw.01G263600' => 'cil', 'CiPaw.02G169100' => 'cil', 'ClCG05G002350' => 'cla', 'ClCG05G002360' => 'cla', 'ClCG06G000460' => 'cla', 'COL.COLO4_12528' => 'col', 'Cpa.g.sc18.103' => 'cpa', 'Cpa.g.sc18.104' => 'cpa', 'Cpa.g.sc3.290' => 'cpa', 'Cre02.g080200' => 'cre', 'CsaV3_3G009790' => 'csa', 'CsaV3_3G009800' => 'csa', 'CsaV3_6G006270' => 'csa', 'CSS0003206' => 'camsi', 'CSS0011294' => 'camsi', 'CSS0012627' => 'camsi', 'CSS0019185' => 'camsi', 'CSS0023997' => 'camsi', 'CSS0048837' => 'camsi', 'DCAR_006424' => 'dca', 'DCAR_008552' => 'dca', 'DCAR_020201' => 'dca', 'DCAR_026638' => 'dca', 'DCAR_031520' => 'dca', 'Dinv22969' => 'din', 'Dinv28547' => 'din', 'Dinv32367' => 'din', 'Dinv43692' => 'din', 'Dinv43694' => 'din', 'Duzib133G1018' => 'dzi', 'Duzib133G1401' => 'dzi', 'Duzib138G0139' => 'dzi', 'Duzib150G1025' => 'dzi', 'ECA233G5874' => 'eca', 'ECA236G2516' => 'eca', 'ECA236G3299' => 'eca', 'ECA238G2900' => 'eca', 'EL10Ac1g00872' => 'bvu', 'EL10Ac2g02445' => 'bvu', 'EL10Ac3g05807' => 'bvu', 'EL10Ac7g17656' => 'bvu', 'Eucgr.D02466' => 'egr', 'Eucgr.D02467' => 'egr', 'Eucgr.I00435' => 'egr', 'Eucgr.J01078' => 'egr', 'FAN01G1392' => 'fan', 'FAN03G2056' => 'fan', 'FAN03G3383' => 'fan', 'FAN06G1243' => 'fan', 'FAN06G5055' => 'fan', 'FAN10G0703' => 'fan', 'FAN10G0988' => 'fan', 'FvH4_7g11500' => 'fve', 'FvH4_7g11510' => 'fve', 'Glyma.03G027500' => 'gma', 'Glyma.03G027600' => 'gma', 'Glyma.10G293500' => 'gma', 'Glyma.20G243500' => 'gma', 'Gohir.A07G146400' => 'ghi', 'Gohir.A08G135700' => 'ghi', 'Gohir.A11G080100' => 'ghi', 'Gohir.A12G101400' => 'ghi', 'Gohir.D07G152500' => 'ghi', 'Gohir.D08G156500' => 'ghi', 'Gohir.D11G084800' => 'ghi', 'Gohir.D12G104400' => 'ghi', 'Gorai.001G174600' => 'gra', 'Gorai.004G162800' => 'gra', 'Gorai.007G090400' => 'gra', 'Gorai.008G113400' => 'gra', 'Gorai.008G113500' => 'gra', 'GSVIVG01016247001' => 'vvi', 'GSVIVG01018555001' => 'vvi', 'GSVIVG01027665001' => 'vvi', 'GSVIVG01027667001' => 'vvi', 'HanXRQChr04g0122721' => 'han', 'HanXRQChr06g0177891' => 'han', 'HanXRQChr08g0223551' => 'han', 'HanXRQChr16g0532481' => 'han', 'HanXRQChr16g0532531' => 'han', 'Haze_16860' => 'cav', 'Haze_26750' => 'cav', 'Hma1.2p1_0044F.1_g026120' => 'hma', 'Hma1.2p1_0301F.1_g118600' => 'hma', 'HPP92_018406' => 'vpl', 'HPP92_022100' => 'vpl', 'HPP92_025679' => 'vpl', 'Hund11801' => 'sun', 'Hund17029' => 'sun', 'Hund17030' => 'sun', 'Lalb_Chr02g0143801' => 'lal', 'Lalb_Chr07g0189921' => 'lal', 'Lalb_Chr07g0189931' => 'lal', 'Lalb_Chr19g0127331' => 'lal', 'Lalb_Chr21g0307101' => 'lal', 'Lj1A983T45' => 'lonja', 'Lj3g0016539' => 'lja', 'Lj3g0018034' => 'lja', 'Lj5g0000937' => 'lja', 'Lj7A531T52' => 'lonja', 'Lj7A531T53' => 'lonja', 'Lsat_1_v5_gn_3_132321' => 'lsa', 'Lsat_1_v5_gn_7_9580' => 'lsa', 'Lsat_1_v5_gn_7_9600' => 'lsa', 'Manes.05G047000' => 'mes', 'Manes.07G098000' => 'mes', 'Manes.11G109100' => 'mes', 'Mapoly0013s0012' => 'mpo', 'Mapoly0114s0015' => 'mpo', 'MBI12_g20322_MAGBIO' => 'mbi', 'MBI12_g20323_MAGBIO' => 'mbi', 'MBI12_g20324_MAGBIO' => 'mbi', 'MBI18_g41468_MAGBIO' => 'mbi', 'MBI18_g41754_MAGBIO' => 'mbi', 'MBI18_g46181_MAGBIO' => 'mbi', 'MCO16G291' => 'mco', 'MD02G1207000' => 'mdo', 'MD02G1207100' => 'mdo', 'MD02G1207200' => 'mdo', 'MD07G1119400' => 'mdo', 'MD07G1119500' => 'mdo', 'Medtr0776s0010' => 'mtr', 'Medtr1g116120' => 'mtr', 'Medtr4g024630' => 'mtr', 'Medtr4g024850' => 'mtr', 'Medtr4g111780' => 'mtr', 'Medtr5g059410' => 'mtr', 'MELO3C006200.2' => 'cme', 'MELO3C006201.2' => 'cme', 'MELO3C022495.2' => 'cme', 'Migut.B01619' => 'egut', 'Migut.B01620' => 'egut', 'Migut.F01973' => 'egut', 'MSTRG.17175' => 'ama', 'MSTRG.20739' => 'ama', 'MSTRG.20740' => 'ama', 'Nitab4.5_0000071g0180' => 'nta', 'Nitab4.5_0001153g0160' => 'nta', 'Nitab4.5_0001329g0110' => 'nta', 'Nitab4.5_0001329g0130' => 'nta', 'Nitab4.5_0003912g0020' => 'nta', 'Nitab4.5_0003912g0060' => 'nta', 'Nitab4.5_0005868g0010' => 'nta', 'Nitab4.5_0007307g0020' => 'nta', 'Nn1g01135' => 'nnu', 'Nn1g01138' => 'nnu', 'Nn4g26364' => 'nnu', 'Oeu005799.2' => 'oeu', 'Oeu005800.1' => 'oeu', 'Oeu031334.1' => 'oeu', 'Oeu055502.1' => 'oeu', 'Os01g0578000' => 'osa', 'Os04g0266900' => 'osa', 'Os06g0133800' => 'osa', 'Peaxi162Scf00238g00810' => 'pax', 'Peaxi162Scf00959g00125' => 'pax', 'Peaxi162Scf00959g00213' => 'pax', 'Peaxi162Scf01227g00027' => 'pax', 'Peaxi162Scf01227g00034' => 'pax', 'PGR004G0700' => 'pgr', 'PGR042G0240' => 'pgr', 'PGR042G1557' => 'pgr', 'PGR044G1518' => 'pgr', 'PGSC0003DMG400007019' => 'stu', 'PGSC0003DMG400007020' => 'stu', 'PGSC0003DMG400014756' => 'stu', 'PGSC0003DMG400022088' => 'stu', 'Phvul.003G037400' => 'pvu', 'Phvul.007G006600' => 'pvu', 'Phvul.010G082100' => 'pvu', 'Potri.002G146300' => 'ptr', 'Potri.010G224600' => 'ptr', 'Potri.014G068100' => 'ptr', 'Potri.014G068200' => 'ptr', 'Pp3c10_10220' => 'ppa', 'Pp3c10_10680' => 'ppa', 'Pp3c15_10830' => 'ppa', 'Pp3c5_12400' => 'ppa', 'Pp3c5_1370' => 'ppa', 'Pp3c9_3690' => 'ppa', 'PRCOL_00003537' => 'pco', 'PRCOL_00005284' => 'pco', 'Prupe.2G143400' => 'ppe', 'Prupe.2G143600' => 'ppe', 'Psat0s4330g0040' => 'psa', 'Psat5g139960' => 'psa', 'Psat6g238800' => 'psa', 'Psat7g230880' => 'psa', 'PSO339G0438' => 'pso', 'PSO478G1820' => 'pso', 'PSO782G0784' => 'pso', 'PSO782G2880' => 'pso', 'PSO832G0911' => 'pso', 'QL08p052781' => 'qlo', 'QL08p052789' => 'qlo', 'QL08p055320' => 'qlo', 'RcHm_v2.0_Chr1g0349891' => 'rch', 'RcHm_v2.0_Chr1g0349941' => 'rch', 'RcHm_v2.0_Chr1g0349951' => 'rch', 'Rhsim03G0169800' => 'rsi', 'Rhsim03G0170000' => 'rsi', 'Rhsim04G0189700' => 'rsi', 'Rhsim04G0189800' => 'rsi', 'Rhsim07G0028800' => 'rsi', 'Rhsim07G0028900' => 'rsi', 'Sabra02G0113900' => 'sbr', 'Sabra10G0173600' => 'sbr', 'Sabra14G0047800' => 'sbr', 'SalBow5G0090' => 'sbo', 'SalBow5G0448' => 'sbo', 'SalBow5G4377' => 'sbo', 'SalBow5G5288' => 'sbo', 'Sc23g0003680' => 'sci', 'Sc23g0003690' => 'sci', 'Sc25g0000120' => 'sci', 'Sed0000766' => 'sed', 'Sed0003578' => 'sed', 'Sed0028009' => 'sed', 'SEGI_02891' => 'sgi', 'SEGI_03178' => 'sgi', 'SEGI_22011' => 'sgi', 'SEGI_32248' => 'sgi', 'SEGI_35236' => 'sgi', 'SEGI_38072' => 'sgi', 'SGA_v2.0_scaffold153G36995' => 'sas', 'SGA_v2.0_scaffold153G36996' => 'sas', 'SGA_v2.0_scaffold95G28908' => 'sas', 'SGA_v2.0_scaffold95G28909' => 'sas', 'SMO259G0042' => 'smo', 'SMO270G0103' => 'smo', 'Solyc01g018020.3' => 'sly', 'Solyc05g050950.2' => 'sly', 'Solyc05g050960.4' => 'sly', 'Solyc05g050970.4' => 'sly', 'Solyc10g018300.3' => 'sly', 'Sopen01g014140' => 'spe', 'Sopen05g029430' => 'spe', 'Sopen05g029440' => 'spe', 'Sopen10g007500' => 'spe', 'Sp4g27300' => 'spa', 'Sp4g27310' => 'spa', 'Sp5g02500' => 'spa', 'Sp6g00180' => 'spa', 'SpUn0031_0010' => 'spa', 'SpUn0031_0020' => 'spa', 'TAR374G0718' => 'tar', 'TAR375G0905' => 'tar', 'TAR375G1132' => 'tar', 'TAR629G2158' => 'tar', 'TAR633G1695' => 'tar', 'THA.LOC104802453' => 'tha', 'THA.LOC104815243' => 'tha', 'THA.LOC104817238' => 'tha', 'THA.LOC104817240' => 'tha', 'Thecc.01G378700' => 'tca', 'Thecc.01G378800' => 'tca', 'Thecc.10G076900' => 'tca', 'Thhalv10001334m.g' => 'esa', 'Thhalv10001529m.g' => 'esa', 'Thhalv10001556m.g' => 'esa', 'Thhalv10005892m.g' => 'esa', 'Thhalv10006511m.g' => 'esa', 'TPR.G10408' => 'tpr', 'TPR.G31325' => 'tpr', 'TPR.G31327' => 'tpr', 'TWI14G0061' => 'twi', 'TWI14G0433' => 'twi', 'TWI59G0361' => 'twi', 'TWI60G0706' => 'twi', 'unitig_0.g1300' => 'ugi', 'unitig_0.g1301' => 'ugi', 'vmacro06777' => 'vma', 'vmacro13414' => 'vma', 'vmacro13415' => 'vma', 'VMungo0331G0509' => 'vmu', 'VMungo0331G1707' => 'vmu', 'VMungo0720G1071' => 'vmu', 'VMungo1215G3274' => 'vmu', 'Zm00001eb086870' => 'zma', 'Zm00001eb160270' => 'zma', 'Zm00001eb378030' => 'zma', 'Zm00001eb389880' => 'zma' ) $gf_id = 'HOM05D001546' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001546' ) $data_identifier = 'HOM05D001546' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 10, 'amhyb' => (int) 4, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 3, 'col' => (int) 1, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 7, 'fve' => (int) 2, 'gma' => (int) 4, 'ghi' => (int) 8, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 2, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 6, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 4, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389880' $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